I disagree! The PZ villians had lost their powers. Yes, they swore they'd regain them, but so what. Villians always swear such things! What Superman did was an execution, AND HE SHOULD NOT HAVE DONE THAT! Superman also killed Doomsday, but I had no problem with that. SM was in the heat of battle with the brute, and he was injured and weakening fast. There was only one way to stop him, and SM did it.
You certainly have a right to express your opinion, and I respect that. However, I think what you're failing to see is the fact that the incident involving the Phantom Zone villains was an extreme case. And Superman was, no matter how you slice it, the last living representative of law and order on Superboy's "pocket universe" Earth. That means there was no one else to refer to, or to defer to. Superman was backed into a corner and had to act alone because there was literally nobody else to back him up or to advise him. We're taking about the murder of an entire planet's biosphere (people, animals, plants, insects, sea life, the whole ball of wax). Zod and his two flunkies rendered an entire planet completely lifeless without any thought of remorse whatsoever. How could Superman, as a law enforcement officer, allow these three to live given the scope of their crime (their power level is pretty much irrelivent in this case)? The case of Superman killing Doomsday was much the same as the case of the Phantom Zone villains when one looks at it. In both cases, Superman had no choice but to do what he did. Doomsday represented a threat to life and limb of such magnetude that he had to be stopped ... by
any means necessary. The case of the Phantom Zone villains is identical (it doesn't matter if they were on a murderous rampage at the time or not). The deed had already been done. The mass-murder of Superboy's adopted home had already been committed. And I say again, Superman had absolutely no other recourse than to execute his duty as the last representative of the law on that world.